Context: Although trauma research has advanced immensely, the struggle to find effective treatment for posttraumatic survivors continues. It seems reasonable to say that, at present, our ability to treat those suffering from posttraumatic stress disorder (PTSD) is, at the very least, limited. Problem: We argue that in order to confront the current crisis in the study of trauma - evidenced by our limited ability to offer successful treatment for those who develop PTSD - we must return to the subjective experience. Our claim is that only by applying a rigorous method to study the subjective experience will we be able to understand the meaning of neuronal activity associated with PTSD. Method: The neurophenomenological research program (NRP) is a working plan that enables us to create a solid and reliable link between the subjective experience and neuronal activity. Thus, the NRP allows us to (a) delve deeply (and rigorously) into the subjective experience and, by so doing, (b) extract the cognitive mechanism that constitutes the building blocks bridging between the subjective experience and neuronal activity. Following this, we will be able to (c) identify the relevant neuronal activity for the phenomenon under examination. Results: Based on previous studies among posttraumatic survivors, we suggest that two cognitive mechanisms are especially relevant for the study of trauma: the sense of body ownership (i.e., the sense that this is our own body) and the sense of agency (the sense that we control our body. The trade-off between these closely related, yet independent mechanisms is highly significant. We conclude the article with the presentation of a detailed working plan for the study of trauma - one that begins with the subject and returns to the subject. Implications: This article summarizes our struggle to conduct a phenomenological research in the study of trauma and our methodological efforts of the last ten years. It should help the beginner to avoid some mistakes that have been made in this long journey, yet obviously, each one must build their own route. Likewise, we suggest that phenomenologists, brain scientists and clinicians should find a way to cooperate. This shared effort might allow us to improve our understanding of the traumatic experience and its long-term implications; as such, we believe that in this process a better treatment could be developed. That being said, the limitation of our proposal is the difficulty of creating a shared language that bridges these different worlds. Constructivist content: We strongly embraces phenomenological approach together with enactivist/embodied theories.